How to Test for the Novel Coronavirus

by Jane SmithMay 13, 2020

How to Test for the Novel Coronavirus

Coronavirus disease 2019 (COVID-19) has taken the world by storm, infecting millions of people, and as of the end of April 2020, killing hundreds of thousands. It is generally agreed that the spread of the disease, which is caused by infection by a virus called SARS-CoV-2, would be slowed if we were better at identifying those who were infected.

There are several issues that complicate the process of diagnosing people with COVID-19, including the fact that many people who have been infected do not have symptoms and so do not seek care from healthcare professionals or engage in measures to prevent themselves from spreading the virus to others. The scarcity of tests for COVID-19 has also been widely cited as a major challenge in dealing with the virus, potentially preventing even those who are deemed likely to have the disease from confirming their diagnosis and clarifying their best courses of action.

Today, the primary way that patients are tested for COVID-19 is through tests that identify the virus based on its genetic code. However, these tests had to be rapidly developed once the virus was detected and do not work perfectly. New tests continue to be developed in the hopes of improving our ability to accurately identify the virus and to do so rapidly, conveniently, and cost-effectively.

Why did we need a specific test for COVID-19?

Because the symptoms of COVID-19 are non-specific, meaning that they do not only occur with COVID-19 but also with other conditions, such as pneumonia, the virus was not immediately recognized as novel. Before we were broadly aware of COVID-19, people who were infected were often diagnosed with pneumonia based on their symptoms - which can vary but often include cough, shortness of breath, and fever - as well as what medical images showed was going on in these patients’ lungs.

Upon suspecting pneumonia, healthcare providers often used an imaging technique known as computed tomography – or CT – to image the lungs and discovered areas of opaqueness in the lungs that led them to assume patients were suffering from pneumonia. However, when these clinicians tested patients for well-known pathogens that could cause pneumonia, those with COVID-19 tested negative.

The inability to identify reasonable causes for pneumonia in these patients led experts to suspect that many patients who appeared to have pneumonia were instead suffering from something else, so they analyzed samples from the lower respiratory systems of these patients to try to determine what could be causing the observed respiratory distress. Through this method, researchers discovered that these patient were infected with a pathogen that, from a genomic standpoint, had a lot in common with known coronaviruses, such as severe acute respiratory syndrome (SARS-CoV) and Middle East respiratory syndrome virus (MERS-CoV).

The novel coronavirus was given the name SARS-CoV-2, and molecular techniques were developed to identify the virus. These tests were needed because clinicians could not make a reliable diagnosis based on symptoms and CT results. They instead needed a way to reveal the specific existence of the pathogen in patients. By January 10th, 2020, the genome sequence of SARS-CoV-2 had been disclosed and added to the GenBank repository. This information has formed the basis for the majority of tests that have been performed on patients to date.

Nucleic Acid Tests are Widely Used to Test for COVID-19

China has approved at least 11 tests for COVID-19 that are based on nucleic acid testing, which represents the principal method for identifying COVID-19. Nucleic acid refers to genetic material like DNA and RNA. The nucleic acid tests for COVID-19 employ a method called reverse transcription polymerase chain reaction, or RT-PCR, to convert the virus’ RNA (which is the basis for the genetic code of SARS-CoV-2) to DNA and to amplify it so that we can identify whether SARs-Co-V is present in a patient sample.

The RT-PCR process can be completed in one-step or two-steps, each of which has its advantages and disadvantages. With the one-step process, testing is more efficiently completed, but less of the DNA needed to identify the virus is created. The two-step process overcomes this latter issue, making it a more sensitive way to identify COVID-19, but this technique is more laborious, and results take longer with two steps. The United States Centers for Disease Control and Prevention (CDC) identifies the virus using the one-step method.

To increase the speed of diagnosis afforded by the current nucleic acid tests for COVID-19, scientists are currently developing new kinds of nucleic acid tests that do not require as much specialized equipment. These types of nucleic acid tests include distinct types of what are called isothermal amplification, meaning that the tests are carried out at a specific temperature. The specific techniques are known as helicase-dependent amplification, recombinase polymerase amplification, and loop-mediation isothermal amplification. Further research on these techniques will help to determine if nucleic acid tests could be valuable for point-of-care diagnosis – a major goal of the World Health Organization.

But All Nucleic Acid Tests Have Some Weaknesses

Experts have pointed to the rate of false-negatives – or cases where infected patients are tested for COVID-19, but the test fails to find the virus – as a significant weakness of nucleic acid tests. The CDC has published information on the potential for false-negatives, and researchers have begun to report on case studies where false-negatives have occurred.

There are concerns over how false-negative results may undermine efforts to slow the spread of the novel coronavirus. Indeed, if the tests that we use to diagnose infected patients miss the virus and lead us to mistakenly label infected people as non-infected, then these people are less likely to be quarantined or to take precautions to ensure that they do not give the virus to others in their environments.

Researchers have therefore begun investigating other methods that could be used to help improve the reliability with which we can diagnose COVID-19. One recent study has shown that supplementing the nucleic acid tests that are already largely employed with tests for specific proteins – called antibodies – could improve our ability to identify COVID-19 and to prevent its spread.

Protein Tests May Offer New Value for Diagnosing COVID-19

Antibodies are proteins that are found in the blood that attack toxins or foreign substances. When something dangerous or foreign enters our bodies, our immune systems identify these entities based on antigens, which tend to be present on the outside of these substances. Based on the molecular structure of these antigens, our immune systems make antibodies to bind to those antigens and eliminate them from the body.

Given that our bodies produce antibodies upon infection, tests for antibodies can often be used as an indirect way of identifying a virus. These tests for antibodies are often referred to as serological tests, as the development of antibodies is called seroconversion.

The new study into the potential of using antibodies to diagnose COVID-19 involved an analysis of data from 173 of the initial 368 COVID-19 patients admitted to the Shenzhen Third People’s Hospital. These patients had all tested positive for COVID-19 using a nucleic acid test. Scientists also tested these patients for certain types of antibodies, known as Immunoglobulin M (IgM) and Immunoglobulin G (IgG), as well as total antibody using a test known as enzyme linked immunosorbent assay (ELISA).

Interestingly, each of the patients who were tested about a month after they were infected had detectable antibodies in their samples, though the antibodies showed up at different times. On average, total antibody became detectable at 11 days, whereas IgM and IgG became detectable at 12 and 14 days after disease onset, respectively. Though samples from 12 patients did not show antibodies, the samples from these patients were from early on after the patients were infected, so the researchers concluded that those patients may not yet have developed antibodies.

This idea that the patients had not yet developed the antibodies was consistent with other observations the scientists made. For instance, the nucleic acid test appeared better at identifying COVID-19 during the first 8 days after disease onset, but the antibody test was better at diagnosing the disease after 8 days. The antibody test was also able to pick up false negatives produced by the nucleic acid tests not only from 8 days after symptoms appeared and later but also as early as one day into the disease.

Another interesting finding of this study was that levels of antibodies after 12 days following disease onset was associated with disease severity. Specifically, patients with higher levels of antibodies in their systems during this time period were more likely to be in critical condition than those with lower levels of antibodies. To date, we have known that older age and male sex are risk factors for the disease, as people in these categories tend to fare worse when infected. These new findings suggest that higher antibody levels may be another factor that can be used to predict details of the course of the disease in infected patients.

But Protein Tests Also Have Weaknesses

As with nucleic acid tests, certain issues related to antibody tests have also been raised. For instance, these tests if used alone could lead to false negatives if used soon after infection, before antibodies have developed. Similarly, details of sample collection and testing procedure may impact the validity of test results.

A relative weakness of antibody protein tests when compared to nucleic acid tests is that there is no approved at-home antibody test to diagnose COVID-19. While the first at-home test for COVID-19 has been approved by the FDA, this test is based on the RT-PCR method and not testing for antibodies.

Some experts also express concern over mistaken assumptions that could arise as a result of antibody testing. With many other viruses, once people have observable levels of antibodies, they may be immune to the virus forever or for some duration. However, we do not yet have enough information on SARS-CoV-2 antibodies to know what kind of immunity to COVID-19 these antibodies may afford.

Takeaway

In the few short months since COVID-19 emerged, two main techniques for diagnosing the disease have developed. One technique is based on identifying the genetic material of the virus in patient samples, whereas the other technique identifies antibodies that the body has developed in response to the virus. The diagnostic tests are evolving, and whether a patient gets a test – and if so, which one – depends on a host of factors including patient symptoms and location, as well as the expert opinion of the patient’s doctor.